canopy.BIC


    list of sampled trees returned by <code><a rd-options="" href="/link/canopy.sample?package=Canopy&version=1.0.0" data-mini-rdoc="Canopy::canopy.sample">canopy.sample</a></code>

sampchain

projectname


    number of MCMC chains with random initiations

numchain

burnin

thin


    whether a pdf plot of BIC should be generated, default to be TRUE


To get BIC as a model selection criterion from MCMC sampling results.


 package

A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase.  When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.

canopy.BIC: To get BIC as a model selection criterion

Description

Usage

Arguments

Value

Examples